Epignetic Cancer project
1 RNA-Seq
1.1 Quality checks
1.1.1 Alignment statistics
1.1.2 PCC replicates
1.1.3 PCA replicates (using norm counts)
1.1.4 GFP reads (genetic system validation)
1.2 Compare GFP and noGFP systems
1.2.1 PCA between conditions (using log2FC)
1.2.2 Overlaps between up and down genes
1.3 MA plots
RNA-Seq differentially expressed genes
1.4 FC up vs down genes per cdition
1.5 Alluvial plots
Visualize transitions between conditions
1.6 Gene overlaps between conditions
1.7 Heatmap logFC genes of interest
1.8 GO up and down genes per condition
2 RNA-Seq clusters analyses
2.1 Cluster figure (heatmap, STRING network, GO, motifs)
2.2 STRING newtork per cluster
2.3 Boxplot quantif FPKM and enrichments
Stratified per cluster and PRC1 binding
2.4 Check percentage of PRC1 bound genes
2.5 Tissue specificity score
Stratified per cluster and PRC1 binding
3 CUTNRUN
3.1 Quality Checks
3.1.1 Alignment statistics
3.1.2 PCC between replicates
3.1.3 PCC between replicates
3.2 MA plots (DESeq2)
4 Reverting vs non reverting genes
4.1 Defining characteristics
4.1.1 FC between conditions
4.1.2 Overlap with RNA clusters
4.1.3 Chromhmm classes
4.1.4 Overlap with K27 and K118 domains
4.1.5 Size of overlapping K27 domains
4.1.6 FPKMs between cditions and percentile
4.1.7 GO
4.1.8 STRING network
4.1.9 Motifs enrichment
4.1.9.1 Over represented motifs
4.1.9.2 Heatmap ZEB and STAT motifs
4.2 Average tracks
4.2.1 Gene promoters PH18/WT conditions
4.2.2 Gene promoters between RNAi condition
4.2.3 PH assigned peaks
PH peaks assigned to their closest gene -> split between recovery & noRecovery
Not used anymore
4.2.4 Compare PH peaks from Science Advances
PH peaks from the Science Advances were used -> aTSS, enhancer, peaks overlapping recovering/non recovering genes promoters